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5.3k
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How to highlight DE genes in plotMD ?
edgeR plotMD volcanoplot mirnaseq
updated 4.4 years ago by • 0 • written 7.4 years ago by ▴ 110
15
votes
7
replies
2.3k
views
6 follow
Forum: What to put in my Github
Github
updated 4.4 years ago by ★ 3.3k • written 4.4 years ago by ▴ 20
0
votes
0
replies
629
views
What criteria follow in order to choose the crystaline structure of a molecule
Molecular Docking
4.4 years ago by roybatty269 • 0
2
votes
2
replies
1.6k
views
Recombination maps for cattle
SNP IMPUTE2 genome Assembly
updated 4.4 years ago by • 0 • written 6.0 years ago by ▴ 10
2
votes
2
replies
1.5k
views
Samtools view filter by reference sequence
samtools
4.4 years ago by maxrwjones ▴ 60
0
votes
0
replies
650
views
The effect of heterozygosity on genome alignment
heterozigosity alignment bwa sequence
4.4 years ago by Iseez • 0
0
votes
2
replies
2.3k
views
Segmentation fault (core dumped) error in MUSCLE
NGS alignment fastq linux sequence
4.4 years ago by steel1990 ▴ 20
0
votes
1
reply
635
views
Genome sequencing data analysis and assembly L.lactis subsp.lactis strain Lac3
well
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
4
votes
1
reply
1.0k
views
Is it bad practice to change threshold for interaction probability?
STRING Cytoscape
updated 4.4 years ago by 9.0k • written 4.4 years ago by ▴ 20
7
votes
8
replies
3.2k
views
bedops wig2bed 'Row begins with a tab or space' error
wig2bed bedops convert2bed
updated 4.4 years ago by 36k • written 4.4 years ago by ▴ 40
0
votes
2
replies
974
views
correlation analysis of a single variable versus multiple variables
correlation r RNA-Seq
4.4 years ago by pinheirofabiano ▴ 130
1
vote
0
replies
629
views
Holistic enzyme activity determination with computation
proteomics protein enzymes
updated 4.2 years ago by 45k • written 4.4 years ago by ▴ 10
0
votes
5
replies
1.3k
views
transcription factor activation order
transcription
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
0
replies
531
views
JoinMap4 makes a new map every time
joinmap linkage_mapping genetic_map SNP
4.4 years ago by Beetle Editor • 0
0
votes
3
replies
3.3k
views
LDSC -Genetic correlation, some results all have NA valuies
correlation ldsc genetic gwas
updated 4.4 years ago by ★ 4.8k • written 4.4 years ago by • 0
0
votes
4
replies
2.1k
views
Can Meta-GWAS summary statistic results be used for Meta-GWAS (For example, METAL)?
METAL input Meta-analysis Meta-GWAS
4.4 years ago by li • 0
4
votes
6
replies
2.0k
views
Batch effect correction of 2 studies with different covariates
batch-effect R RNA-seq
updated 4.4 years ago by ★ 2.9k • written 4.4 years ago by ▴ 20
1
vote
2
replies
1.7k
views
MemoryError w/ matrix | Smith-Waterman Algorithm Python
Python Smith-Waterman
updated 18 months ago by 45k • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Job: Informatician / Data Analyst | University of Glasgow
data-analyst
updated 2.3 years ago by 45k • written 4.4 years ago by 15k
1
vote
3
replies
2.1k
views
IndexError: list assignment index out of range | Needleman-Wunsch Algorithm - Python
Python Needleman-Wunsch Dynamic-Programming
updated 18 months ago by 45k • written 4.4 years ago by ▴ 10
1
vote
2
replies
1.7k
views
Pooling normal data in Mutect2
mutect2 pooling normal samples panelofnormals
4.4 years ago by Michelle • 0
17
votes
4
replies
5.8k
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin samtools bcftools vcf split-vep
updated 3.0 years ago by ▴ 250 • written 4.4 years ago by ★ 4.4k
0
votes
0
replies
1.1k
views
integration of single cell RNA-seq and bulk RNA-seq data
RNA-seq
4.4 years ago by ramyak1912 • 0
3
votes
4
replies
2.0k
views
how to extract REF and ALT DNA string around SNV
SNV motif
4.4 years ago by shangguandong1996 ▴ 30
0
votes
0
replies
576
views
Minimum enrichment score to take for analysis
Sequencing Rna-Seq
4.4 years ago by ashwing.kofficial ▴ 10
0
votes
4
replies
1.9k
views
How to Estimate total variance in, and between RNA-seq datasets?
batch variance correction
4.4 years ago by Gabriel ▴ 180
0
votes
1
reply
907
views
Detection of bacterial SNP using regular PCR primers
detection PCR SNP
updated 4.4 years ago by ▴ 170 • written 4.4 years ago by ▴ 170
3
votes
4
replies
6.4k
views
Can't change coefficient of dds object: error 'coef' should specify same coefficient as in results 'res'
DESeq2 RNA-seq
4.4 years ago by macielrodriguez2 ▴ 50
3
votes
2
replies
1.6k
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 4.4 years ago by 89k • written 4.4 years ago by ★ 4.4k
0
votes
0
replies
799
views
Negative branch length when using clustalw through Python and unable to see bootstrap values
clustalw Phylogeny bootstrap Python tree
4.4 years ago by minifoog ▴ 10
1
vote
3
replies
2.5k
views
About combining the forward and reverse sequence
16srRNA geneious
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
0
votes
0
replies
812
views
<*> meaning in Vcf Output From Mpileup
mpileup missing deletion vcf
4.4 years ago by breezin • 0
4
votes
6
replies
8.2k
views
Fastqc shows over-represented sequence with no sequence given?
sequencing
updated 2.8 years ago by 45k • written 10.2 years ago by ▴ 50
5
votes
3
replies
4.2k
views
how remove large gene ontology terms from gprofiler2 output
gprofiler2 GO DEseq RNA-seq
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.7k
views
Job: R/Shiny web application developer in bioinformatics startup
web visualization shiny
4.4 years ago by ivo.kwee • 0
0
votes
2
replies
3.1k
views
freebayes for snp call in pooled samples: how do I set the parameters?
SNP freebayes pooled ploidy
updated 4.4 years ago by ▴ 10 • written 5.5 years ago by • 0
2
votes
6
replies
2.6k
views
Can't count features with featurecount
RNAseq featurecounts
4.4 years ago by avelarbio46 ▴ 30
1
vote
3
replies
705
views
How do I find the gene name with the allele number from the databases?
rna-seq
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
1
vote
2
replies
1.8k
views
How to implement k fold cv after randomForest
k_fold_cv R randomForest
4.4 years ago by pt.taklifi ▴ 70
4
votes
2
replies
5.1k
views
How to visualize Multiple Sequence Alignment with python ?
python clustalw msa
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
0
votes
0
replies
886
views
Is there a faster way to download gene sequences from NCBI via E-utils
NCBI E-utils Unix
updated 2.5 years ago by 45k • written 4.4 years ago by ▴ 60
0
votes
0
replies
730
views
Job: Postdoc Fellow @ New York City: Alternative Splicing
splicing genomics rnaseq
4.4 years ago by fanggang ▴ 120
2
votes
4
replies
1.7k
views
Finding how many times a nucleotide appear in the same position
Beginer Nucleotide Python DNA
updated 4.4 years ago by 166k • written 4.4 years ago by • 0
1
vote
2
replies
1.4k
views
Taxonomy assignment of viral RNA
assembly taxa metagenomics
4.4 years ago by biobiu ▴ 150
7
votes
12
replies
3.6k
views
RNAseq data analysis of pooled data
DESeq2 mapping featurecounts clustering RNA-Seq
updated 4.4 years ago by ★ 2.6k • written 4.4 years ago by ▴ 130
0
votes
0
replies
686
views
Identify sample mix from NGS data
NGS samplemix contamination celllineauthentication
4.4 years ago by Boberoni ▴ 20
2
votes
1
reply
1.1k
views
CNV-calling single sample
copynumbervariation cnv GATK na12878
updated 20 months ago by ▴ 200 • written 4.4 years ago by ▴ 20
0
votes
0
replies
2.0k
views
Is there any Python or other software that can replace the function "networklevel" in R package "bipartite" for calculation?
R networklevel
4.4 years ago by 153348734 • 0
2
votes
3
replies
1.5k
views
GTF file and Transcript ID
transcriptid rnaseq gtf
updated 4.4 years ago by ★ 2.2k • written 4.4 years ago by ▴ 10
0
votes
1
reply
815
views
Couldnot access BSRD database
database website BSRD
updated 14 months ago by • 0 • written 4.4 years ago by • 0
121,904 results • Page 674 of 2439
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Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Recent Replies
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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